Whole-genome sequence analysis of Nocardioides sp. InS609-2 isolated from Antarctica

Abstract:

[Background] Nocardioides sp. InS609-2 is a potential new strain of polar actinomycete isolated from the soil sample collected from Inexpressible Island in Terra Nova Bay of the Ross Sea, Antarctica. Little is known about the full genome sequence, functional genes, metabolite synthesis pathways, and comparative genomics of Nocardioides sp. InS609-2. [Objective] To explore the genes associated with secondary metabolites from the genome sequence of Nocardioides sp. InS609-2. [Methods] The complete genome map of InS609-2 was sequenced on the Illumina HiSeq platform, followed by read assembly, gene prediction, gene annotation, prediction of gene clusters for secondary metabolite biosynthesis, and synteny analysis. [Results] The full length of the genome was 4 524 052 bp, with the G+C content of 69.42%. A total of 4 656 genes, 56 tRNAs, and 6 rRNAs were predicted. Among them, 3 761, 3 052, 1 767, 4 134, and 2 725 genes were annotated in COG, GO, KEGG, NR, and Swiss-Prot, respectively. Meanwhile, 19 gene clusters for secondary metabolite synthesis were predicted. Genome sequencing data was submitted to NCBI, with the GenBank accession number CP060034. The synteny analysis and protein cluster analysis were performed for Nocardioides sp. InS609-2 together with N. dokdonensis CP015079, N. yefusunii CP034929, N. euryhalodurans CP038267, N. seonyuensis CP038436, N. daphniae CP038462, and N. okcheonensis CP087710. The results showed both conserved and unique regions among the seven genomes. The seven genomes shared 44 protein clusters. Finally, the 16S rRNA gene-based phylogenetic analysis, pan genome analysis, core genome analysis, and genome-based phylogenetic analysis were carried out to further mine the genomic information of Nocardioides sp. InS609-2. [Conclusion] This study provides reference information for predicting the gene clusters involved in secondary metabolite biosynthesis of Nocardioides sp. InS609-2 at the genomic level, which is essential for the subsequent studies of InS609-2.